WO2005083618A3 - Method and apparatus for modelling, simulating and analyzing chemical reactions and biochemical processes - Google Patents

Method and apparatus for modelling, simulating and analyzing chemical reactions and biochemical processes Download PDF

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Publication number
WO2005083618A3
WO2005083618A3 PCT/US2005/005505 US2005005505W WO2005083618A3 WO 2005083618 A3 WO2005083618 A3 WO 2005083618A3 US 2005005505 W US2005005505 W US 2005005505W WO 2005083618 A3 WO2005083618 A3 WO 2005083618A3
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WO
WIPO (PCT)
Prior art keywords
modelling
simulating
chemical reactions
biochemical processes
simulation engine
Prior art date
Application number
PCT/US2005/005505
Other languages
French (fr)
Other versions
WO2005083618A2 (en
Inventor
Roy Lurie
Joseph F Hicklin
Ricardo E Paxson
Edward Whittington Gulley
Original Assignee
Mathworks Inc
Roy Lurie
Joseph F Hicklin
Ricardo E Paxson
Edward Whittington Gulley
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Mathworks Inc, Roy Lurie, Joseph F Hicklin, Ricardo E Paxson, Edward Whittington Gulley filed Critical Mathworks Inc
Priority to EP05713895A priority Critical patent/EP1721281A2/en
Priority to JP2006554277A priority patent/JP4852430B2/en
Publication of WO2005083618A2 publication Critical patent/WO2005083618A2/en
Publication of WO2005083618A3 publication Critical patent/WO2005083618A3/en

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Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/10—Analysis or design of chemical reactions, syntheses or processes
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • G16B5/30—Dynamic-time models
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Abstract

A system for modifying a model of a chemical reaction or biochemical process responsive to experimental results generated by an in situ experiment conducted on an experimental platform includes a simulation engine and an analysis environment. The simulation engine generates an expected result from a model of the chemical reaction or biochemical process. The analysis environment communicates with the simulation engine, gathers data from an experimental platform, and compares the expected result to data gathered from the platform.
PCT/US2005/005505 2004-02-20 2005-02-18 Method and apparatus for modelling, simulating and analyzing chemical reactions and biochemical processes WO2005083618A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP05713895A EP1721281A2 (en) 2004-02-20 2005-02-18 Method and apparatus for modelling, simulating and analyzing chemical reactions and biochemical processes
JP2006554277A JP4852430B2 (en) 2004-02-20 2005-02-18 Method and apparatus for facilitating communication with a simulation environment

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US10/783,522 US8554486B2 (en) 2004-02-20 2004-02-20 Method, computer program product, and apparatus for selective memory restoration of a simulation
US10/783,522 2004-02-20

Publications (2)

Publication Number Publication Date
WO2005083618A2 WO2005083618A2 (en) 2005-09-09
WO2005083618A3 true WO2005083618A3 (en) 2006-05-26

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2005/005505 WO2005083618A2 (en) 2004-02-20 2005-02-18 Method and apparatus for modelling, simulating and analyzing chemical reactions and biochemical processes

Country Status (5)

Country Link
US (1) US8554486B2 (en)
EP (1) EP1721281A2 (en)
JP (1) JP4852430B2 (en)
CN (1) CN1942878A (en)
WO (1) WO2005083618A2 (en)

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US20070150254A1 (en) * 2005-12-23 2007-06-28 Choi Cathy Y Simulation engine for a performance validation system
US7729894B1 (en) * 2006-05-12 2010-06-01 The Mathworks, Inc. Test postcondition items for automated analysis and test generation
US8234623B2 (en) 2006-09-11 2012-07-31 The Mathworks, Inc. System and method for using stream objects to perform stream processing in a text-based computing environment
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US8005812B1 (en) 2007-03-16 2011-08-23 The Mathworks, Inc. Collaborative modeling environment
US9729843B1 (en) 2007-03-16 2017-08-08 The Mathworks, Inc. Enriched video for a technical computing environment
AU2009281721A1 (en) * 2008-08-15 2010-02-18 Merrimack Pharmaceuticals, Inc. Methods and systems for predicting response of cells to a therapeutic agent
US8285523B2 (en) * 2009-02-17 2012-10-09 Massachusetts Institute Of Technology Electronic system for modeling chemical reactions and biochemical processes
NZ602084A (en) 2010-03-11 2014-07-25 Merrimack Pharmaceuticals Inc Use of erbb3 inhibitors in the treatment of triple negative and basal-like breast cancers
TWI437390B (en) 2011-01-07 2014-05-11 Ind Tech Res Inst Hybrid simulation system and method
US10521521B2 (en) * 2013-10-14 2019-12-31 Aveva Software, Llc Shared repository of simulation models
US10437210B2 (en) * 2013-10-14 2019-10-08 Aveva Software, Llc Interactive feedback for variable equation specifications
US10339231B2 (en) * 2013-10-14 2019-07-02 Schneider Electric Software, Llc Entity type templates in process simulation
WO2015100459A2 (en) 2013-12-27 2015-07-02 Merrimack Pharmaceuticals, Inc. Biomarker profiles for predicting outcomes of cancer therapy with erbb3 inhibitors and/or chemotherapies
US10332619B2 (en) 2014-10-13 2019-06-25 Samsung Electronics Co., Ltd. Methods and apparatus for in silico prediction of chemical reactions
CN107787466A (en) * 2015-04-29 2018-03-09 通用电气健康护理生物科学股份公司 The system and method for user's visualized management directly perceived for the automation of bioprocess
US10184006B2 (en) 2015-06-04 2019-01-22 Merrimack Pharmaceuticals, Inc. Biomarkers for predicting outcomes of cancer therapy with ErbB3 inhibitors
US11880292B2 (en) * 2016-02-17 2024-01-23 Micro Focus Llc Environment simulations
WO2018035718A1 (en) * 2016-08-23 2018-03-01 Accenture Global Solutions Limited Real-time industrial plant production prediction and operation optimization
US11183273B2 (en) * 2017-09-01 2021-11-23 X Development Llc Heterogeneous method for modelling a biochemical environment
EP3566769B1 (en) * 2018-05-07 2023-07-26 Yf1 Method and device for simulating an industrial facility for exploiting a chemical or biochemical method
US10586362B2 (en) * 2018-06-18 2020-03-10 Microsoft Technology Licensing, Llc Interactive layout-aware construction of bespoke charts
EP3591543B1 (en) * 2018-07-03 2023-09-06 Yf1 System and method for simulating a chemical or biochemical process
US11500528B2 (en) * 2019-07-01 2022-11-15 Palantir Technologies Inc. System architecture for cohorting sensor data

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Also Published As

Publication number Publication date
US20050187745A1 (en) 2005-08-25
US8554486B2 (en) 2013-10-08
JP4852430B2 (en) 2012-01-11
EP1721281A2 (en) 2006-11-15
CN1942878A (en) 2007-04-04
WO2005083618A2 (en) 2005-09-09
JP2007534318A (en) 2007-11-29

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